Variant report

Variant	rs3748612
Chromosome Location	chr1:151742798-151742799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151738680..151741094-chr1:151741696..151744217,2	K562	blood:
2	chr1:151739594..151742008-chr1:151742708..151744217,2	K562	blood:

Variant related genes	Relation type
ENSG00000143450	Chromatin interaction
ENSG00000268288	Chromatin interaction
ENSG00000249602	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10888435	0.88[CEU][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes]
rs11204885	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11204887	0.93[EUR][1000 genomes]
rs11204888	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12066445	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12073999	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12409493	0.88[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs12567867	0.90[EUR][1000 genomes]
rs1781419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293088	0.88[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs33911740	0.93[EUR][1000 genomes]
rs3923394	0.96[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs4845572	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6667279	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6679233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7534811	0.88[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs868868	0.82[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9017	0.84[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs9826	0.88[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3748612	TDRKH	Cis_1M	lymphoblastoid	RTeQTL
rs3748612	TDRKH	cis	cerebellum	SCAN
rs3748612	S100A13	cis	cerebellum	SCAN
rs3748612	BCL9	cis	cerebellum	SCAN
rs3748612	LINGO4	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151736600-151746200	Weak transcription	Thymus	Thymus
2	chr1:151736600-151746600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:151736600-151751000	Weak transcription	Ovary	ovary
4	chr1:151736800-151745400	Weak transcription	Fetal Brain Female	brain
5	chr1:151736800-151745800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr1:151736800-151745800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:151736800-151745800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:151736800-151746000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:151736800-151746000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:151736800-151746200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:151736800-151746200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:151736800-151746200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:151736800-151746200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:151736800-151746200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:151736800-151746200	Weak transcription	Fetal Thymus	thymus
16	chr1:151736800-151746400	Weak transcription	Aorta	Aorta
17	chr1:151736800-151746400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:151736800-151746400	Weak transcription	Right Ventricle	heart
19	chr1:151736800-151746600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:151736800-151746600	Weak transcription	Psoas Muscle	Psoas
21	chr1:151736800-151746800	Weak transcription	Left Ventricle	heart
22	chr1:151736800-151746800	Weak transcription	Spleen	Spleen
23	chr1:151736800-151747200	Weak transcription	Fetal Brain Male	brain
24	chr1:151736800-151747400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:151736800-151747800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:151736800-151748000	Weak transcription	Colonic Mucosa	Colon
27	chr1:151736800-151750800	Weak transcription	Right Atrium	heart
28	chr1:151736800-151762600	Weak transcription	Gastric	stomach
29	chr1:151737000-151743000	Weak transcription	Primary T cells from cord blood	blood
30	chr1:151737000-151745200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:151737000-151745400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:151737000-151745600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:151737000-151745800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:151737000-151745800	Weak transcription	Liver	Liver
35	chr1:151737000-151745800	Weak transcription	Brain Germinal Matrix	brain
36	chr1:151737000-151745800	Weak transcription	Brain Substantia Nigra	brain
37	chr1:151737000-151746000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:151737000-151746000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:151737000-151746200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:151737000-151746200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:151737000-151746400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:151737000-151746400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:151737000-151746400	Weak transcription	Brain Angular Gyrus	brain
44	chr1:151737000-151746400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:151737000-151746400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:151737000-151746400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:151737000-151746400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:151737000-151746400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:151737000-151746400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:151737000-151746600	Weak transcription	Fetal Muscle Leg	muscle

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